Features and default color

Hi everyone,

I have 2 questions :

does somebody know if it is possible when launching the applet online to give it parameters so that the default coloring would be the coloring of an attached annotation file ?
As far as I have seen from the applet's parameter list, it is not, but maybe someone knows a trick to do it ?

And I also wanted to ask : is it possible to activate specific features by clicking on an annotation line ? So imagine there is 3 or 4 annotation lines, but they only concern part of the sequence list.
Would it be possible to highlight/select/color the sequences related to this annotation line ?

Thank you in advance,

Balazs

Hi Balazs,

Hi everyone,

I have 2 questions :

does somebody know if it is possible when launching the applet online to give it parameters so that the default coloring would be the coloring of an attached annotation file ?
As far as I have seen from the applet's parameter list, it is not, but maybe someone knows a trick to do it ?

This functionality was actually suggested back in 2008 by Darron Handley in an email to the list (http://issues.jalview.org/browse/JAL-333) - unfortunately, nothing has been done about extending the annotation file format or the JalviewLite api to support it yet. The fix didn't make it in to Jalview 2.5, and I've had a few too many other distractions.

And I also wanted to ask : is it possible to activate specific features by clicking on an annotation line ? So imagine there is 3 or 4 annotation lines, but they only concern part of the sequence list.
Would it be possible to highlight/select/color the sequences related to this annotation line ?

If you have sequence or group associated annotation, then Jalview will highlight the associated IDs if you click on the annotation row's label, and select the associated sequences if you double click. However, this may not be what you want - would you like to create a feature request over at issues.jalview.org ?

I plan to revise the underlying datamodel for features and annotations over the next few (or more) months, and it's good to know of any additional situations that I might be able to implement support for.

Jim.

ยทยทยท

On 19/11/2010 16:06, Balazs Laurenczy wrote:

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